The pilot whales were stranded after the worst mass beaching in the country's history.
Japanese authorities have rescued a second survivor as they race to find dozens of missing sailors from a cargo ship that sank in a typhoon.
Authorities blamed the incident on unlawful fishing, as they seized over 100 km of illegal fishing nets since January.
As they return to the seas for the first time since April, rescue ship operators say migrants fleeing Libya's humanitarian crisis are undeterred by Europe's coronavirus outbreak
News of the missing boat comes amid criticism of the European Union's lack of rescue missions in the Mediterranean Sea.
The coastguard saved 149 people, including 13 women and three children, from a ship that sank on Saturday.
The 47-year old woman was floating in a rubber dinghy in the Aegean Sea for nearly two days before she was rescued by Greek coast guards.
"We are extremely relieved to finally bring the remaining 88 exhausted and traumatised rescued persons to a safe port soon," said German NGO Sea-Eye.
The situation aboard Ocean Viking puts EU's new plan to distribute migrants to the test.
The migrants were picked up in two separate operations off the coast of Libya, MSF, who runs the ship alongside SOS Mediterranee, said on Twitter.